Zinc in PDB 6xpd: Cryo-Em Structure of Human ZNT8 Double Mutant - D110N and D224N, Determined in Outward-Facing Conformation

The binding sites of Zinc atom in the Cryo-Em Structure of Human ZNT8 Double Mutant - D110N and D224N, Determined in Outward-Facing Conformation (pdb code 6xpd). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Cryo-Em Structure of Human ZNT8 Double Mutant - D110N and D224N, Determined in Outward-Facing Conformation, PDB code: 6xpd:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Cryo-Em Structure of Human ZNT8 Double Mutant - D110N and D224N, Determined in Outward-Facing Conformation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Cryo-Em Structure of Human ZNT8 Double Mutant - D110N and D224N, Determined in Outward-Facing Conformation within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:0.1 occ:1.00 OE1 B:GLU352 1.8 68.0 1.0 NE2 B:HIS301 1.9 60.5 1.0 ND1 B:HIS318 1.9 57.7 1.0 SG A:CYS53 2.5 88.2 1.0 CE1 B:HIS318 2.8 57.7 1.0 CD B:GLU352 2.8 68.0 1.0 CD2 B:HIS301 2.9 60.5 1.0 CE1 B:HIS301 2.9 60.5 1.0 CG B:HIS318 3.1 57.7 1.0 CE1 A:HIS54 3.2 88.5 1.0 OE2 B:GLU352 3.2 68.0 1.0 NE2 A:HIS54 3.3 88.5 1.0 CB B:HIS318 3.5 57.7 1.0 NE2 B:HIS318 3.9 57.7 1.0 ND1 B:HIS301 4.0 60.5 1.0 CG B:HIS301 4.0 60.5 1.0 CD2 B:HIS318 4.1 57.7 1.0 ND1 A:HIS54 4.1 88.5 1.0 CG B:GLU352 4.1 68.0 1.0 O A:HIS52 4.2 92.3 1.0 CB A:CYS53 4.3 88.2 1.0 CD2 A:HIS54 4.4 88.5 1.0 O A:CYS53 4.6 88.2 1.0 OE1 B:GLN350 4.6 50.1 1.0 CG A:HIS54 4.8 88.5 1.0

Zinc binding site 2 out of 4 in the Cryo-Em Structure of Human ZNT8 Double Mutant - D110N and D224N, Determined in Outward-Facing Conformation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Cryo-Em Structure of Human ZNT8 Double Mutant - D110N and D224N, Determined in Outward-Facing Conformation within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:0.8 occ:1.00 SG B:CYS364 2.0 81.3 1.0 ND1 A:HIS54 2.0 88.5 1.0 SG B:CYS361 2.5 99.6 1.0 CE1 A:HIS54 2.5 88.5 1.0 CA B:CYS361 2.7 99.6 1.0 CB B:CYS361 2.7 99.6 1.0 NE2 A:HIS52 2.8 92.3 1.0 CE1 A:HIS52 2.9 92.3 1.0 CG A:HIS54 2.9 88.5 1.0 O B:CYS361 3.5 99.6 1.0 C B:CYS361 3.5 99.6 1.0 NE2 A:HIS54 3.5 88.5 1.0 CB A:HIS54 3.6 88.5 1.0 CB B:CYS364 3.7 81.3 1.0 CD2 A:HIS54 3.7 88.5 1.0 N B:CYS361 3.8 99.6 1.0 CD2 A:HIS52 4.0 92.3 1.0 N B:CYS364 4.1 81.3 1.0 ND1 A:HIS52 4.1 92.3 1.0 O B:ASP360 4.3 99.5 1.0 CA B:CYS364 4.4 81.3 1.0 C B:ASP360 4.4 99.5 1.0 N B:LEU362 4.7 93.9 1.0 CG A:HIS52 4.7 92.3 1.0 C B:CYS364 4.7 81.3 1.0 C B:PHE363 5.0 91.1 1.0 N B:PHE363 5.0 91.1 1.0 O B:CYS364 5.0 81.3 1.0

Zinc binding site 3 out of 4 in the Cryo-Em Structure of Human ZNT8 Double Mutant - D110N and D224N, Determined in Outward-Facing Conformation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Cryo-Em Structure of Human ZNT8 Double Mutant - D110N and D224N, Determined in Outward-Facing Conformation within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:0.8 occ:1.00 OE1 A:GLU352 1.5 68.5 1.0 ND1 A:HIS318 1.8 58.4 1.0 NE2 A:HIS301 1.8 60.6 1.0 CD A:GLU352 2.6 68.5 1.0 SG B:CYS53 2.7 89.2 1.0 CE1 A:HIS301 2.8 60.6 1.0 CE1 A:HIS318 2.8 58.4 1.0 CG A:HIS318 2.8 58.4 1.0 CD2 A:HIS301 2.9 60.6 1.0 OE2 A:GLU352 3.1 68.5 1.0 CB A:HIS318 3.2 58.4 1.0 CE1 B:HIS54 3.5 89.8 1.0 NE2 B:HIS54 3.7 89.8 1.0 CG A:GLU352 3.8 68.5 1.0 NE2 A:HIS318 3.9 58.4 1.0 ND1 A:HIS301 3.9 60.6 1.0 CD2 A:HIS318 3.9 58.4 1.0 CG A:HIS301 4.0 60.6 1.0 O B:HIS52 4.4 93.9 1.0 OE1 A:GLN350 4.4 50.5 1.0 CB B:CYS53 4.5 89.2 1.0 ND1 B:HIS54 4.5 89.8 1.0 CA A:HIS318 4.7 58.4 1.0 CD2 B:HIS54 4.8 89.8 1.0 O B:CYS53 4.9 89.2 1.0 CB A:GLU352 5.0 68.5 1.0

Zinc binding site 4 out of 4 in the Cryo-Em Structure of Human ZNT8 Double Mutant - D110N and D224N, Determined in Outward-Facing Conformation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Cryo-Em Structure of Human ZNT8 Double Mutant - D110N and D224N, Determined in Outward-Facing Conformation within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:0.5 occ:1.00 SG A:CYS364 2.0 82.5 1.0 ND1 B:HIS54 2.1 89.8 1.0 SG A:CYS361 2.5 0.6 1.0 CE1 B:HIS54 2.6 89.8 1.0 CA A:CYS361 2.6 0.6 1.0 CB A:CYS361 2.7 0.6 1.0 NE2 B:HIS52 2.8 93.9 1.0 CE1 B:HIS52 2.9 93.9 1.0 CG B:HIS54 3.0 89.8 1.0 C A:CYS361 3.4 0.6 1.0 O A:CYS361 3.5 0.6 1.0 NE2 B:HIS54 3.6 89.8 1.0 CB B:HIS54 3.6 89.8 1.0 CB A:CYS364 3.7 82.5 1.0 N A:CYS361 3.7 0.6 1.0 CD2 B:HIS54 3.8 89.8 1.0 CD2 B:HIS52 4.0 93.9 1.0 N A:CYS364 4.1 82.5 1.0 ND1 B:HIS52 4.1 93.9 1.0 O A:ASP360 4.3 0.9 1.0 CA A:CYS364 4.4 82.5 1.0 C A:ASP360 4.4 0.9 1.0 N A:LEU362 4.6 94.8 1.0 CG B:HIS52 4.7 93.9 1.0 C A:CYS364 4.8 82.5 1.0 N A:PHE363 4.9 92.5 1.0 C A:PHE363 4.9 92.5 1.0

J.Xue, T.Xie, W.Zeng, Y.Jiang, X.C.Bai. Cryo-Em Structures of Human ZNT8 in Both Outward- and Inward-Facing Conformations. Elife V. 9 2020.
ISSN: ESSN 2050-084X
PubMed: 32723473
DOI: 10.7554/ELIFE.58823